The Step Up:
A great exercise to prevent knee pain, strengthen the glutes and hip flexors. It does a great job of balancing both sides of the body, many times one side is much stronger than the other side. There are several types of step ups out there and I perform several varieties with my patients. Here is a great version to help strengthen the hip flexors for the runner as well strengthen the inside of the knee.
How to perform: As you step up you will want to keep the weight on your heel as well as point your toes upward, this will put the emphasis on the glutes, inside thigh, and hip flexors, next bring the rear leg upward, again pointing your toe and foot upward to get maximum activation of the hip flexors. Perform a total of 8-12 reps per leg (depending on your ability and form.)
Be careful when adding weight, the most important aspect of the exercise is form, typically people use too much weight too fast and this results in poor form, the goal is to get the most "bang for your buck". The goal is to build a great base of strength in the inside quad and hip flexors, lots of weight is not needed.
Add this to your lower body routine to build a solid foundation of structural balance.
Here is a great article explaining Patello Femoral Pain and some great stretches and exercises